Computational protocol: Population genetic structure of the major malaria vector Anopheles funestus s.s. and allied species in southern Africa

Similar protocols

Protocol publication

[…] The DNA sequence data were aligned in Bioedit 7.0.9 []. The sequences were deposited in GenBank under accession numbers JQ424478-JQ424787. Sequence polymorphism and nucleotide divergence with Jukes and Cantor distance (K) statistics were estimated using DnaSP 5.0 []. Phylogenetic relationships for construction of a haplotype network were assessed using the statistical parsimony method implemented in TCS version 1.21 []. Neighbor-Joining (NJ) analysis was conducted using MEGA 4.0 []. Node support for NJ result was assessed using 1000 bootstrap pseudo-replicates. To find which substitution model best described the evolution of concatenated ND5 and COI sequences, Modeltest [] was used to perform a hierarchical likelihood ratio test. The Tamura Nei model [] was specified for concatenated ND5 and COI sequences using the Akaike information criterion. The model, TIM3 + I + G was used for maximum likelihood analysis using PhyML 3.0 []. The primer sequences were not added to the analysis due to unclear primer sequence data from some of specimens although the results were not affected. […]

Pipeline specifications

Software tools BioEdit, DnaSP, MEGA, ModelTest-NG, PhyML
Application Phylogenetics
Organisms Anopheles funestus
Diseases Coloboma, Malaria
Chemicals Nucleotides